MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20)

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

% Affected Genes	Class Size (#genes)	Average Regulation (ratio)	Class	Accession	Would Be Affected (#genes)	affected	Class	Microarray Measured (#genes)

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

% Affected Genes	Class Size (#genes)	Average Regulation (ratio)	Class	Would Be Affected (#genes)
6.3492	142	2.1655175536870956	protein amino acid dephosphorylation	9
5.7692	117	2.6894871592521667	muscle development	7
5.7143	158	2.1655175536870956	dephosphorylation	9
5.1546	107	2.329086923599243	embryonic morphogenesis	6
5.0000	226	2.6329536702897816	response to cold	11
4.7244	142	1.632481078306834	mitosis	7
4.7059	216	2.4113256633281708	response to freezing	10
4.6784	217		homoiothermy
4.4554	249	2.6329536702897816	response to temperature stimulus	11
4.4444	226	2.4113256633281708	thermoregulation	10
4.3573	535	1.8484420895576477	regulation of progression through cell cycle	23
4.3197	539		regulation of cell cycle
3.9773	192	2.6829177481787547	regulation of growth	8
3.9735	164	2.267966568470001	transmembrane receptor protein tyrosine kinase signaling pathway	7
3.8095	230	2.3925783783197403	enzyme linked receptor protein signaling pathway	9
3.7234	208	1.8230999537876673	RNA splicing	8
3.5604	746	1.8924930147502734	cell cycle process	27
3.4335	264	2.2164768129587173	organ morphogenesis	9
3.4146	229	1.6467143297195435	cell cycle phase	8
3.3333	170	1.3052469968795777	regulation of cell differentiation	6
3.2258	378	2.3798144817352296	alcohol metabolic process	12
3.0968	890	2.4829982866843543	phosphate metabolic process	28
			phosphorus metabolic process
3.0405	1721	2.470501118236118	protein modification process	52
3.0303	222	1.3425244291623433	cell division	7
	458	1.6056334376335144	cell cycle	14
3.0060	1226	2.403050871690114	response to stress	37
2.9801	338	2.3975469536251492	positive regulation of transcription	10
2.9680	499	2.46775693159837	regulation of transcription from RNA polymerase II promoter	15
2.9529	1442	2.4479837675352356	post-translational protein modification	43
2.9412	195	2.9956377029418944	chromatin modification	6
2.9393	1780	2.470501118236118	biopolymer modification	52
2.9289	318	2.6086528982434953	inflammatory response	9
2.9197	358	2.4850547462701797	response to wounding	10
2.9070	206	2.844642996788025	nucleocytoplasmic transport	6
2.8939	347	2.3975469536251492	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	10
2.8736	416	2.530326783657074	response to abiotic stimulus	12
2.8646	443	2.5862315134568648	ubiquitin cycle	13
2.8333	686	2.1418599311043236	anatomical structure morphogenesis	19
2.8249	211	2.7829527854919434	visual perception	6
2.8090	212		sensory perception of light stimulus
2.7174	231	3.0316067695617677	microtubule-based process
2.6820	1217	2.7678764888218472	intracellular signaling cascade	33
2.6596	229	1.6556044340133667	anion transport	6
2.6362	1588	2.630213709672292	transcription	42
2.6247	429	2.28793443441391	positive regulation of cellular metabolic process	11
2.6245	2628	2.3178554457061145	regulation of transcription	69
2.6235	768	2.3607054107329426	protein transport	20
2.6201	735	2.6820639967918396	immune response	19
2.6103	1273	2.1811264465595115	anatomical structure development	33

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.